Display a pseudo-image of a microarray chip

Description

Produces a pseudo-image (graphics::image) for each sample.

Usage

## S4 method for signature 'FeatureSet'
image(x, which, transfo=log2, ...)

## S4 method for signature 'PLMset'
image(x, which=0,
                   type=c("weights","resids", "pos.resids","neg.resids","sign.resids"),
                   use.log=TRUE, add.legend=FALSE, standardize=FALSE,
                   col=NULL, main, ...)

Arguments

Examples

if(require(oligoData) & require(pd.hg18.60mer.expr)){
  data(nimbleExpressionFS)
  par(mfrow=c(1, 2))
  image(nimbleExpressionFS, which=4)
##  fit <- fitPLM(nimbleExpressionFS)
##  image(fit, which=4)
  plot(1) ## while fixing fitPLM TODO
}

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.

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Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(oligo)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: oligoClasses
Welcome to oligoClasses version 1.34.0
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: Biostrings
Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
================================================================================
Welcome to oligo version 1.36.1
================================================================================
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/oligo/image.Rd_%03d_medium.png", width=480, height=480)
> ### Name: image
> ### Title: Display a pseudo-image of a microarray chip
> ### Aliases: image image-methods image,FeatureSet-method
> ###   image,PLMset-method
> ### Keywords: hplot
> 
> ### ** Examples
> 
> if(require(oligoData) & require(pd.hg18.60mer.expr)){
+   data(nimbleExpressionFS)
+   par(mfrow=c(1, 2))
+   image(nimbleExpressionFS, which=4)
+ ##  fit <- fitPLM(nimbleExpressionFS)
+ ##  image(fit, which=4)
+   plot(1) ## while fixing fitPLM TODO
+ }
Loading required package: oligoData
Loading required package: pd.hg18.60mer.expr
Loading required package: RSQLite
Loading required package: DBI
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>